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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ), 'gf_id' => 'HOM05D001206', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001206' ), 'data_identifier' => 'HOM05D001206', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001206', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p33990' => 'bna', 'A02p43320' => 'bna', 'A06p31100' => 'bna', 'A09p24920' => 'bna', 'Aa31LG1G17460' => 'aar', 'Aa31LG2G6650' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.369' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.411' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1093' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1898' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2068' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2069' => 'aag', 'Actinidia00325' => 'ach', 'Actinidia00326' => 'ach', 'Actinidia02414' => 'ach', 'Actinidia11180' => 'ach', 'Actinidia12826' => 'ach', 'Actinidia16517' => 'ach', 'Actinidia25415' => 'ach', 'Ah.01g007260' => 'amhyb', 'Ah.01g016080' => 'amhyb', 'Ah.01g024200' => 'amhyb', 'Ah.02g117670' => 'amhyb', 'AL5G14200' => 'aly', 'AL8G41810' => 'aly', 'Aqoxy3G00674' => 'aox', 'Aqoxy425s001' => 'aox', 'Aqoxy6G00228' => 'aox', 'Aqoxy6G00631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02U3XB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3DT0RH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FS28A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53RDS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.66L233' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZT8G9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXFN4R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J66KI7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRA1N7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NWD6TW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZY648K' => 'arhy', 'AT3G25660' => 'ath', 'AT5G64440' => 'ath', 'ATR0584G074' => 'atr', 'ATR0584G155' => 'atr', 'ATR0800G073' => 'atr', 'ATR1096G083' => 'atr', 'Atru.chr4.1112' => 'acertr', 'Atru.chr6.3565' => 'acertr', 'AUR62000552' => 'cqu', 'AUR62004905' => 'cqu', 'AUR62006904' => 'cqu', 'AUR62027076' => 'cqu', 'AUR62030916' => 'cqu', 'AUR62032754' => 'cqu', 'BcaB06g27855' => 'bca', 'BcaB07g29744' => 'bca', 'BcaB07g30259' => 'bca', 'BcaB07g30635' => 'bca', 'BcaB07g32014' => 'bca', 'BcaB07g32016' => 'bca', 'BcaC01g02682' => 'bca', 'BcaC01g06941' => 'bca', 'BcaC03g15127' => 'bca', 'BcaC03g17284' => 'bca', 'BcaC03g18264' => 'bca', 'BcaC04g21423' => 'bca', 'BcaC04g22258' => 'bca', 'BcaC05g25894' => 'bca', 'BolC2t12406H' => 'bol', 'BolC3t18443H' => 'bol', 'BolC9t56049H' => 'bol', 'BraA02t08420Z' => 'bra', 'BraA02t08421Z' => 'bra', 'BraA02t09258Z' => 'bra', 'BraA06t26053Z' => 'bra', 'BraA09t38080Z' => 'bra', 'C02p52310' => 'bna', 'C02p63380' => 'bna', 'C03p61790' => 'bna', 'C03p61820' => 'bna', 'C05p18490' => 'bna', 'C09p31950' => 'bna', 'CAN.G1191.9' => 'can', 'CAN.G504.50' => 'can', 'CAN.G504.51' => 'can', 'CAN.G504.52' => 'can', 'CAN.G504.53' => 'can', 'CAN.G504.54' => 'can', 'CANSAT01G2722' => 'cansat', 'CANSAT54G1477' => 'cansat', 'CANSAT64G1074' => 'cansat', 'CARHR260190' => 'chi', 'CARHR278410' => 'chi', 'CARHR288520' => 'chi', 'Carub.0005s0348' => 'cru', 'Carub.0008s2524' => 'cru', 'Ca_00185_v3' => 'car', 'Ca_14632_v3' => 'car', 'Ca_17001_v3' => 'car', 'Ca_17610_v3' => 'car', 'CBR_g12438' => 'cbr', 'CBR_g31867' => 'cbr', 'CBR_g36483' => 'cbr', 'CBR_g41054' => 'cbr', 'Cc00_g12090' => 'ccan', 'Cc02_g20550' => 'ccan', 'Cc05_g09120' => 'ccan', 'CDE04G3774' => 'cde', 'CDE05G0826' => 'cde', 'CDE05G3011' => 'cde', 'CDE07G0825' => 'cde', 'Cfa001628' => 'cfa', 'Cfa002167' => 'cfa', 'Cfa004794' => 'cfa', 'Cfa022689' => 'cfa', 'Cfa023711' => 'cfa', 'Cfa026647' => 'cfa', 'Cfa027295' => 'cfa', 'Ciclev10001093m.g' => 'ccl', 'Ciclev10002998m.g' => 'ccl', 'Ciclev10014821m.g' => 'ccl', 'CiPaw.03G115500' => 'cil', 'CiPaw.03G196100' => 'cil', 'CiPaw.04G077300' => 'cil', 'CiPaw.05G026300' => 'cil', 'CiPaw.05G026500' => 'cil', 'ClCG04G001740' => 'cla', 'ClCG09G016410' => 'cla', 'ClCG09G022260' => 'cla', 'COL.COLO4_12112' => 'col', 'Cpa.g.c43323' => 'cpa', 'Cpa.g.sc139.29' => 'cpa', 'Cpa.g.sc20.48' => 'cpa', 'Cpa.g.sc37.38' => 'cpa', 'Cre02.g103350' => 'cre', 'Cre10.g439400' => 'cre', 'CsaV3_4G030810' => 'csa', 'CsaV3_7G007390' => 'csa', 'CSS0000304' => 'camsi', 'CSS0001960' => 'camsi', 'CSS0014076' => 'camsi', 'CSS0017124' => 'camsi', 'CSS0023121' => 'camsi', 'CSS0045489' => 'camsi', 'CSS0046406' => 'camsi', 'CSS0050390' => 'camsi', 'DCAR_005658' => 'dca', 'DCAR_009614' => 'dca', 'DCAR_013291' => 'dca', 'DCAR_019960' => 'dca', 'DCAR_029282' => 'dca', 'Dinv06275' => 'din', 'Dinv08963' => 'din', 'Dinv40958' => 'din', 'Duzib147G0233' => 'dzi', 'Duzib187G1023' => 'dzi', 'Duzib248G0450' => 'dzi', 'Duzib264G0587' => 'dzi', 'ECA233G3159' => 'eca', 'ECA233G4817' => 'eca', 'ECA234G3918' => 'eca', 'ECA236G0460' => 'eca', 'ECA248G2477' => 'eca', 'EL10Ac4g09666' => 'bvu', 'EL10Ac9g21024' => 'bvu', 'EL10Ac9g22131' => 'bvu', 'Eucgr.I00054' => 'egr', 'Eucgr.I02568' => 'egr', 'Eucgr.I02569' => 'egr', 'Eucgr.I02570' => 'egr', 'Eucgr.K01190' => 'egr', 'FAN02G0831' => 'fan', 'FAN06G1107' => 'fan', 'FAN09G4419' => 'fan', 'FAN10G2392' => 'fan', 'FAN11G2548' => 'fan', 'FAN14G2675' => 'fan', 'FAN15G0254' => 'fan', 'FAN18G2655' => 'fan', 'FAN19G1240' => 'fan', 'FAN21G1587' => 'fan', 'FAN23G0439' => 'fan', 'FAN24G1517' => 'fan', 'FAN25G3564' => 'fan', 'FAN26G0547' => 'fan', 'FAN26G0979' => 'fan', 'FAN26G1265' => 'fan', 'FAN27G1668' => 'fan', 'FAN28G1033' => 'fan', 'FAN28G2051' => 'fan', 'FvH4_1g25540' => 'fve', 'FvH4_2g11120' => 'fve', 'FvH4_4g03380' => 'fve', 'FvH4_4g05790' => 'fve', 'FvH4_4g16160' => 'fve', 'FvH4_5g31820' => 'fve', 'FvH4_6g33420' => 'fve', 'FvH4_6g37630' => 'fve', 'FvH4_7g03390' => 'fve', 'Glyma.04G207800' => 'gma', 'Glyma.05G195500' => 'gma', 'Glyma.06G158000' => 'gma', 'Glyma.08G003100' => 'gma', 'Glyma.08G311400' => 'gma', 'Glyma.13G254200' => 'gma', 'Glyma.15G060700' => 'gma', 'Glyma.18G104200' => 'gma', 'Gohir.A05G382400' => 'ghi', 'Gohir.A06G169500' => 'ghi', 'Gohir.A10G067900' => 'ghi', 'Gohir.A11G058000' => 'ghi', 'Gohir.A12G017600' => 'ghi', 'Gohir.A13G049200' => 'ghi', 'Gohir.D01G147500' => 'ghi', 'Gohir.D04G032800' => 'ghi', 'Gohir.D05G115500' => 'ghi', 'Gohir.D06G177200' => 'ghi', 'Gohir.D07G172800' => 'ghi', 'Gohir.D10G107300' => 'ghi', 'Gohir.D11G062200' => 'ghi', 'Gohir.D12G018200' => 'ghi', 'Gohir.D13G047700' => 'ghi', 'Gorai.004G133000' => 'gra', 'Gorai.005G091000' => 'gra', 'Gorai.007G067000' => 'gra', 'Gorai.008G018500' => 'gra', 'Gorai.010G111500' => 'gra', 'Gorai.010G208200' => 'gra', 'Gorai.011G117700' => 'gra', 'Gorai.012G037200' => 'gra', 'Gorai.013G053300' => 'gra', 'Gorai.N005800' => 'gra', 'Gorai.N008100' => 'gra', 'GSVIVG01020788001' => 'vvi', 'GSVIVG01022368001' => 'vvi', 'GSVIVG01038529001' => 'vvi', 'HanXRQChr01g0018901' => 'han', 'HanXRQChr04g0113591' => 'han', 'HanXRQChr08g0227101' => 'han', 'HanXRQChr08g0227111' => 'han', 'HanXRQChr10g0291231' => 'han', 'HanXRQChr13g0387351' => 'han', 'HanXRQChr15g0469241' => 'han', 'HanXRQChr15g0469251' => 'han', 'Haze_10389' => 'cav', 'Haze_13462' => 'cav', 'Haze_13465' => 'cav', 'Haze_25341' => 'cav', 'Haze_25342' => 'cav', 'Haze_27080' => 'cav', 'Hma1.2p1_0134F.1_g061460' => 'hma', 'Hma1.2p1_0178F.1_g078230' => 'hma', 'Hma1.2p1_0908F.1_g235710' => 'hma', 'Hma1.2p1_0908F.1_g235720' => 'hma', 'Hma1.2p1_2077F.1_g313360' => 'hma', 'Hma1.2p1_2302F.1_g319310' => 'hma', 'Hma1.2p1_3358F.1_g335550' => 'hma', 'HPP92_002350' => 'vpl', 'HPP92_002388' => 'vpl', 'HPP92_004400' => 'vpl', 'HPP92_017097' => 'vpl', 'HPP92_017107' => 'vpl', 'HPP92_027806' => 'vpl', 'Hund00402' => 'sun', 'Hund07212' => 'sun', 'Hund07738' => 'sun', 'Lalb_Chr11g0068731' => 'lal', 'Lalb_Chr12g0202931' => 'lal', 'Lalb_Chr12g0202941' => 'lal', 'Lalb_Chr15g0080441' => 'lal', 'Lalb_Chr20g0122751' => 'lal', 'Lj1A587G24' => 'lonja', 'Lj1g0004459' => 'lja', 'Lj1g0004545' => 'lja', 'Lj1g0006094' => 'lja', 'Lj1g0024754' => 'lja', 'Lj2C608G9' => 'lonja', 'Lj4g0025003' => 'lja', 'Lj5A225G70' => 'lonja', 'Lj6g0018418' => 'lja', 'Lj6g0027071' => 'lja', 'Lj9A342T54' => 'lonja', 'Lsat_1_v5_gn_1_81601' => 'lsa', 'Lsat_1_v5_gn_5_110881' => 'lsa', 'Lsat_1_v5_gn_5_180321' => 'lsa', 'Lsat_1_v5_gn_5_69021' => 'lsa', 'Lsat_1_v5_gn_7_83060' => 'lsa', 'Lsat_1_v5_gn_7_90360' => 'lsa', 'Lsat_1_v5_gn_8_31840' => 'lsa', 'Manes.01G129100' => 'mes', 'Manes.10G094600' => 'mes', 'Manes.13G079500' => 'mes', 'Mapoly0001s0333' => 'mpo', 'Mapoly0029s0077' => 'mpo', 'Mapoly0056s0114' => 'mpo', 'MBI05_g35447_MAGBIO' => 'mbi', 'MBI16_g16199_MAGBIO' => 'mbi', 'MBI16_g44751_MAGBIO' => 'mbi', 'MBI18_g28046_MAGBIO' => 'mbi', 'MCO01G356' => 'mco', 'MCO11G436' => 'mco', 'MD05G1050200' => 'mdo', 'MD09G1156700' => 'mdo', 'MD15G1139000' => 'mdo', 'MD17G1143200' => 'mdo', 'Medtr2g010180' => 'mtr', 'Medtr3g048950' => 'mtr', 'Medtr3g096980' => 'mtr', 'Medtr8g066660' => 'mtr', 'Medtr8g094740' => 'mtr', 'MELO3C008949.2' => 'cme', 'MELO3C014457.2' => 'cme', 'MELO3C018563.2' => 'cme', 'Migut.B00517' => 'egut', 'Migut.H00836' => 'egut', 'Migut.H02113' => 'egut', 'MSTRG.12835' => 'ama', 'MSTRG.16638' => 'ama', 'MSTRG.20250' => 'ama', 'MSTRG.2774' => 'ama', 'Nitab4.5_0000120g0190' => 'nta', 'Nitab4.5_0000323g0050' => 'nta', 'Nitab4.5_0001277g0070' => 'nta', 'Nitab4.5_0001277g0080' => 'nta', 'Nitab4.5_0001402g0110' => 'nta', 'Nitab4.5_0001402g0160' => 'nta', 'Nitab4.5_0002027g0090' => 'nta', 'Nitab4.5_0002335g0070' => 'nta', 'Nitab4.5_0006854g0050' => 'nta', 'Nitab4.5_0006854g0060' => 'nta', 'Nitab4.5_0009020g0080' => 'nta', 'Nitab4.5_0010352g0070' => 'nta', 'Nitab4.5_0010352g0080' => 'nta', 'Nn1g01395' => 'nnu', 'Nn1g05689' => 'nnu', 'Nn1g08806' => 'nnu', 'Nn5g28308' => 'nnu', 'Nn6g34432' => 'nnu', 'Nn7g37382' => 'nnu', 'Oeu032122.1' => 'oeu', 'Oeu041088.1' => 'oeu', 'Oeu042318.2' => 'oeu', 'Oeu059886.1' => 'oeu', 'Os04g0102700' => 'osa', 'Os04g0643200' => 'osa', 'Os11g0170000' => 'osa', 'Os12g0169000' => 'osa', 'Peaxi162Scf00016g03464' => 'pax', 'Peaxi162Scf00035g03126' => 'pax', 'Peaxi162Scf00152g00738' => 'pax', 'Peaxi162Scf00299g00236' => 'pax', 'Peaxi162Scf00310g00515' => 'pax', 'Peaxi162Scf00310g00516' => 'pax', 'Peaxi162Scf00310g00521' => 'pax', 'PGR119G1042' => 'pgr', 'PGR142G2427' => 'pgr', 'PGR142G3322' => 'pgr', 'PGR142G3443' => 'pgr', 'PGSC0003DMG400003119' => 'stu', 'PGSC0003DMG400003120' => 'stu', 'PGSC0003DMG400011995' => 'stu', 'PGSC0003DMG400045238' => 'stu', 'PGSC0003DMG401003118' => 'stu', 'PGSC0003DMG401021239' => 'stu', 'PGSC0003DMG402003118' => 'stu', 'PGSC0003DMG402021239' => 'stu', 'Phvul.002G275700' => 'pvu', 'Phvul.006G036200' => 'pvu', 'Phvul.006G199100' => 'pvu', 'Phvul.009G152300' => 'pvu', 'Potri.001G285900' => 'ptr', 'Potri.005G070300' => 'ptr', 'Potri.007G098600' => 'ptr', 'Potri.018G086350' => 'ptr', 'Pp3c10_23960' => 'ppa', 'Pp3c11_9200' => 'ppa', 'Pp3c16_16670' => 'ppa', 'Pp3c23_9920' => 'ppa', 'Pp3c26_13660' => 'ppa', 'Pp3c27_1950' => 'ppa', 'Pp3c3_2980' => 'ppa', 'Pp3c7_18330' => 'ppa', 'Pp3s32_288' => 'ppa', 'PRCOL_00000262' => 'pco', 'PRCOL_00005592' => 'pco', 'PRCOL_00005593' => 'pco', 'PRCOL_00006355' => 'pco', 'Prupe.3G169900' => 'ppe', 'Prupe.4G282000' => 'ppe', 'Prupe.4G282100' => 'ppe', 'Prupe.8G076300' => 'ppe', 'Psat1g212600' => 'psa', 'Psat5g059040' => 'psa', 'Psat5g186880' => 'psa', 'Psat7g043520' => 'psa', 'PSO017G2524' => 'pso', 'PSO108G0001' => 'pso', 'PSO170G4632' => 'pso', 'PSO478G1473' => 'pso', 'PSO528G0179' => 'pso', 'PSO700G0067' => 'pso', 'PSO761G0240' => 'pso', 'QL08p043357' => 'qlo', 'QL10p040090' => 'qlo', 'QL11p026734' => 'qlo', 'RcHm_v2.0_Chr2g0123671' => 'rch', 'RcHm_v2.0_Chr2g0133671' => 'rch', 'RcHm_v2.0_Chr2g0150631' => 'rch', 'RcHm_v2.0_Chr6g0269381' => 'rch', 'RcHm_v2.0_Chr7g0228001' => 'rch', 'Rhsim05G0095600' => 'rsi', 'Rhsim05G0097400' => 'rsi', 'Rhsim05G0097600' => 'rsi', 'Rhsim05G0098400' => 'rsi', 'Rhsim06G0124000' => 'rsi', 'Rhsim07G0133900' => 'rsi', 'Rhsim08G0002000' => 'rsi', 'Rhsim08G0139700' => 'rsi', 'Sabra07G0082000' => 'sbr', 'Sabra07G0082200' => 'sbr', 'Sabra16G0178300' => 'sbr', 'Sabra16G0178400' => 'sbr', 'SalBow6G5084' => 'sbo', 'SalBow7G4591' => 'sbo', 'Sc09g0002170' => 'sci', 'Sc21g0004390' => 'sci', 'Sed0003330' => 'sed', 'Sed0006625' => 'sed', 'Sed0026081' => 'sed', 'SEGI_05956' => 'sgi', 'SEGI_06909' => 'sgi', 'SEGI_08438' => 'sgi', 'SEGI_09922' => 'sgi', 'SEGI_11684' => 'sgi', 'SEGI_12238' => 'sgi', 'SEGI_12357' => 'sgi', 'SEGI_13870' => 'sgi', 'SEGI_17157' => 'sgi', 'SEGI_25123' => 'sgi', 'SEGI_26191' => 'sgi', 'SEGI_32961' => 'sgi', 'SEGI_40749' => 'sgi', 'SGA_v2.0_scaffold20G08966' => 'sas', 'SGA_v2.0_scaffold342G49396' => 'sas', 'SGA_v2.0_scaffold4G02113' => 'sas', 'SMO037G0003' => 'smo', 'SMO117G0062' => 'smo', 'SMO118G0181' => 'smo', 'SMO304G0067' => 'smo', 'SMO347G0405' => 'smo', 'Solyc01g106330.3' => 'sly', 'Solyc01g106340.3' => 'sly', 'Solyc01g106350.4' => 'sly', 'Solyc01g106360.3' => 'sly', 'Solyc10g007840.3' => 'sly', 'Solyc12g068075.1' => 'sly', 'Solyc12g070090.1' => 'sly', 'Sopen01g009080' => 'spe', 'Sopen01g048700' => 'spe', 'Sopen01g048710' => 'spe', 'Sopen01g048720' => 'spe', 'Sopen01g048730' => 'spe', 'Sopen09g020170' => 'spe', 'Sopen10g003740' => 'spe', 'Sopen12g027140' => 'spe', 'Sp2g14920' => 'spa', 'Sp2g27530' => 'spa', 'TAR381G0025' => 'tar', 'TAR628G1628' => 'tar', 'TAR629G1684' => 'tar', 'THA.LOC104799673' => 'tha', 'THA.LOC104804452' => 'tha', 'THA.LOC104805240' => 'tha', 'THA.LOC104819480' => 'tha', 'THA.LOC104824040' => 'tha', 'Thecc.01G141900' => 'tca', 'Thecc.02G124600' => 'tca', 'Thecc.10G113900' => 'tca', 'Thhalv10003835m.g' => 'esa', 'Thhalv10012940m.g' => 'esa', 'Thhalv10017423m.g' => 'esa', 'TPR.G13547' => 'tpr', 'TPR.G14752' => 'tpr', 'TPR.G20838' => 'tpr', 'TPR.G32630' => 'tpr', 'TPR.G33886' => 'tpr', 'TPR.G35165' => 'tpr', 'TPR.G37395' => 'tpr', 'TPR.G39552' => 'tpr', 'TWI14G1249' => 'twi', 'TWI23G1316' => 'twi', 'TWI38G0487' => 'twi', 'TWI75G0035' => 'twi', 'TWI79G0285' => 'twi', 'unitig_21.g20702' => 'ugi', 'unitig_22.g6850' => 'ugi', 'unitig_899.g14643' => 'ugi', 'unitig_899.g14644' => 'ugi', 'vmacro00705' => 'vma', 'vmacro00706' => 'vma', 'vmacro01903' => 'vma', 'vmacro05367' => 'vma', 'vmacro12422' => 'vma', 'vmacro12423' => 'vma', 'vmacro17696' => 'vma', 'vmacro18673' => 'vma', 'vmacro19593' => 'vma', 'VMungo0251G0194' => 'vmu', 'VMungo0540G0597' => 'vmu', 'VMungo0540G1701' => 'vmu', 'VMungo1309G1884' => 'vmu', 'Zm00001eb068770' => 'zma', 'Zm00001eb091740' => 'zma', 'Zm00001eb407850' => 'zma', 'Zm00001eb407860' => 'zma', 'Zm00001eb418940' => 'zma' ) $gf_id = 'HOM05D001206' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001206' ) $data_identifier = 'HOM05D001206' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'aag' => (int) 7, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 2, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 3, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 19, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 13, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 9, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 13, 'sas' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418940' $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